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Sample GSM39904 Query DataSets for GSM39904
Status Public on Feb 21, 2005
Title Diaphragm 0366
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Diaphragm 0366
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-09/20439.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2
UNF_VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 633 608 357 169 276 439 689 627 359 175 332 458 0 0 169 232 68 44 86 92 82 90 715 790 .629 1.591 1.38 1.394 1.42 2.18 52 278 1.551 .8 80 1290 7560 48 56 89 97 0 371 103 268 .97 382 279 1.031 .841 -.044 -.25 -.044
2 583 214 360 172 223 42 613 222 362 177 253 50 0 0 160 63 64 44 88 53 80 19 265 303 5.31 .188 .198 .246 .309 2.501 52 259 .206 .46 80 1430 7560 48 56 103 111 0 130 105 26 .115 135 30 8.708 .121 -3.122 -3.053 -3.122
3 1182 2297 356 166 826 2131 1264 2372 372 197 908 2206 0 0 393 748 89 165 93 100 93 96 2957 3114 .388 2.58 2.43 2.691 2.593 1.344 32 220 2.444 .94 70 1570 7570 49 56 117 124 0 1401 101 1299 1.573 1446 1345 .636 1.481 .654 .567 .654
4 3653 5550 378 187 3275 5363 3741 6037 387 207 3363 5850 0 0 1735 2741 86 141 100 100 98 100 8638 9213 .611 1.638 1.74 1.682 1.663 1.31 52 305 1.63 .98 80 1730 7560 48 56 133 141 0 3384 114 3270 .999 3681 3567 1.001 1.061 -.002 .085 -.002
5 643 784 367 168 276 616 693 884 371 178 326 716 0 0 200 274 70 52 87 87 78 87 892 1042 .448 2.232 2.196 2.05 2.043 1.943 32 165 1.922 .86 60 1870 7570 50 56 148 154 0 478 102 376 1.361 539 437 .735 1.339 .445 .421 .445
6 526 316 335 175 191 141 561 318 334 180 226 143 0 0 140 85 57 43 84 90 81 84 332 369 1.355 .738 .633 .689 .706 1.765 32 176 .563 .69 60 2010 7570 50 56 162 168 0 193 107 86 .45 194 87 2.222 .386 -1.152 -1.374 -1.152
7 715 2333 316 165 399 2168 732 2521 317 170 416 2356 0 0 206 747 56 42 90 100 88 100 2567 2772 .184 5.434 5.663 5.498 5.268 1.434 52 292 5.173 .9 90 2160 7560 47 56 175 184 0 1423 101 1322 3.313 1537 1437 .302 3.453 1.728 1.788 1.728
8 3976 10760 301 157 3675 10603 4155 10881 306 164 3854 10724 0 0 1744 5073 60 49 100 100 100 100 14278 14578 .347 2.885 2.783 2.949 3.017 1.288 52 308 2.932 .98 90 2310 7560 47 56 190 199 0 6561 96 6465 1.759 6635 6539 .568 1.697 .815 .763 .815
9 912 1210 289 149 623 1061 951 1277 294 158 662 1128 0 0 202 309 61 50 100 100 100 100 1684 1790 .587 1.703 1.704 1.737 1.75 1.423 32 219 1.748 .92 70 2450 7560 48 55 205 212 0 738 91 647 1.038 779 688 .963 1.039 .054 .055 .054
10 569 308 303 142 266 166 585 295 302 148 282 153 0 0 162 98 57 38 90 93 87 87 432 435 1.602 .624 .543 .552 .528 1.729 32 165 .503 .74 60 2600 7560 49 55 221 227 0 188 87 101 .381 180 93 2.628 .331 -1.394 -1.596 -1.394
11 1009 1205 303 133 706 1072 991 1086 308 138 688 953 0 0 416 541 60 37 98 98 96 98 1778 1641 .659 1.518 1.385 1.581 1.488 1.618 52 279 1.49 .95 80 2740 7570 49 57 234 242 0 735 81 654 .926 662 581 1.08 .845 -.111 -.244 -.111
12 1162 1255 309 143 853 1112 1205 1269 311 148 896 1126 0 0 312 383 63 44 98 100 98 100 1965 2022 .767 1.304 1.257 1.329 1.265 1.775 52 337 1.284 .94 90 2890 7560 47 56 248 257 0 765 87 678 .795 774 687 1.258 .766 -.331 -.384 -.331
13 894 935 314 153 580 782 902 923 321 155 588 770 0 0 232 300 72 45 96 100 90 96 1362 1358 .742 1.348 1.31 1.402 1.281 1.91 32 207 1.323 .9 70 3040 7570 49 56 264 271 0 570 93 477 .822 563 470 1.216 .798 -.283 -.325 -.283
14 548 267 316 149 232 118 551 289 321 152 235 140 0 0 120 87 68 42 88 75 80 67 350 375 1.966 .509 .596 .458 .569 2.616 52 305 .482 .7 90 3180 7560 47 56 277 286 0 163 91 72 .31 176 85 3.224 .363 -1.689 -1.461 -1.689
15 3116 26044 327 146 2789 25898 3302 28369 329 151 2975 28223 0 0 1728 15844 72 43 98 100 98 100 28687 31198 .108 9.286 9.487 9.314 9.138 1.563 80 373 9.406 .98 100 3330 7560 47 57 292 302 0 15880 89 15791 5.662 17298 17209 .177 5.785 2.501 2.532 2.501
16 1402 4604 331 138 1071 4466 1424 4847 338 142 1093 4709 0 0 372 1332 80 39 98 100 98 100 5537 5802 .24 4.17 4.308 4.276 4.151 1.263 52 319 4.139 .96 90 3470 7560 47 56 306 315 0 2807 84 2723 2.543 2955 2871 .393 2.627 1.346 1.393 1.346
17 523 317 335 137 188 180 548 329 344 141 213 192 0 0 114 101 77 45 87 90 78 87 368 405 1.044 .957 .901 .681 .889 3.159 32 212 .872 .64 70 3620 7580 50 57 322 329 0 193 84 110 .584 201 117 1.713 .55 -.776 -.863 -.776
18 559 263 328 139 231 124 560 265 336 140 232 126 0 0 173 93 66 37 87 84 78 65 355 358 1.863 .537 .543 .64 .513 2.222 32 195 .395 .65 70 3770 7570 49 56 337 344 0 160 85 76 .327 162 77 3.055 .331 -1.611 -1.594 -1.611
19 826 765 322 134 504 631 800 659 327 137 478 525 0 0 297 356 65 37 92 100 88 100 1135 1003 .799 1.252 1.098 1.242 1.244 1.564 52 288 1.247 .92 80 3910 7570 49 57 351 359 0 466 82 385 .763 402 320 1.31 .67 -.389 -.578 -.389
20 564 405 305 141 259 264 547 432 311 144 242 291 0 0 128 106 62 45 90 90 84 90 523 533 .981 1.019 1.202 1.058 1.015 1.964 32 187 .998 .76 70 4070 7570 49 56 367 374 0 247 86 161 .622 263 177 1.609 .733 -.686 -.448 -.686

Total number of rows: 43008

Table truncated, full table size 9455 Kbytes.




Supplementary data files not provided

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